ENH: Bump scilpy to version 1.5.0 and upgrade dependencies

Bump `scilpy` to version 1.5.0 and upgrade dependencies accordingly.

Require the `scilpy`-patched `dipy` version to avoid package
compatibility issues.

Remove the dependencies force-upgrade in the package testing workflow,
as the versions required by `scilpy` are now modern enough to avoid the
primary issues they intended to fix.

Fix the BLAS option warning in `numpy` triggered by `python-spams` when
using an earlier version of `numpy`. Fixes:
```
AttributeError: module 'numpy.__config__' has no attribute 'blas_opt_info'

ERROR: Failed building wheel for python-spams
```

reported in:
https://github.com/scil-vital/tractolearn/actions/runs/4901866945/jobs/8753373506#step:5:945

.github/workflows/check_format.yml

@@ -13,7 +13,7 @@ jobs:
  strategy:
  matrix:
  os: [ubuntu-latest]
- python-version: [3.8]
+ python-version: ['3.10']
  requires: ['latest']
 
  steps:

.github/workflows/issue_title_labeler.yml

@@ -13,7 +13,7 @@ jobs:
  - uses: actions/checkout@v3
  - uses: actions/setup-python@v4
  with:
- python-version: '3.8'
+ python-version: '3.10'
  - name: Install packages
  run: |
  python -m pip install --upgrade --user pip

.github/workflows/pr_title_labeler.yml

@@ -12,7 +12,7 @@ jobs:
  - uses: actions/checkout@v3
  - uses: actions/setup-python@v4
  with:
- python-version: '3.8'
+ python-version: '3.10'
  - name: Install packages
  run: |
  python -m pip install --upgrade --user pip

.github/workflows/test_package.yml

@@ -15,7 +15,7 @@ jobs:
  # max-parallel: 6
  matrix:
  os: [ubuntu-latest]
- python-version: [3.8]
+ python-version: ['3.10']
  requires: ['minimal', 'latest']
 
  steps:
@@ -53,16 +53,6 @@ jobs:
  python -m pip install --upgrade --user pip
  pip install setuptools tox
  pip install -e .[test]
- # Force upgrading packages to workaround the `scilpy` requested versions
- pip install --upgrade matplotlib==3.1.0
- pip install --upgrade numpy==1.23.0
- # Force upgrading packages to avoid numpy-related built-in type deprecation warnings
- pip install --upgrade dipy==1.4.1
- pip install --upgrade fury==0.7.1
- pip install --upgrade h5py==3.0.0
- pip install --upgrade nibabel==3.2.1
- pip install --upgrade scikit-learn==0.24.0
- pip install --upgrade scipy==1.7.0
  python --version
  pip --version
  pip list

.pre-commit-config.yaml

@@ -1,5 +1,5 @@
 default_language_version:
- python: python3.8
+ python: python3.10
 
 repos:
  - repo: https://github.com/pre-commit/pre-commit-hooks

README.md

@@ -17,11 +17,11 @@ Tractography learning.
 ## Installation
 
 To use tractolearn, it is recommended to create a virtual environment using
-python 3.8 that will host the necessary dependencies. Torch tested with an
+python 3.10 that will host the necessary dependencies. Torch tested with an
 NVIDIA RTX 3090 with:
 
 ```sh
- virtualenv tractolearn_env --python=python3.8
+ virtualenv tractolearn_env --python=python3.10
  source tractolearn_env/bin/activate
 ```
 

pyproject.toml

@@ -20,25 +20,25 @@ dependencies = [
  # common dependencies
  "importlib-metadata",
  "comet-ml == 3.0.0",
- "h5py == 2.10.0",
- "matplotlib >= 2.2.0",
- "numpy >= 1.20.0",
+ "h5py == 3.7.0",
+ "matplotlib == 3.6.0",
+ "numpy == 1.23.0",
  "pandas",
  "pathos",
  "pyyaml",
  "seaborn == 0.11.0",
- "scikit-learn == 0.22.0",
- "scipy == 1.4.0",
- "torch == 1.8.1",
+ "scikit-learn == 1.2.0",
+ "scipy == 1.9.0",
+ "torch == 1.13.0",
  "torchsummary == 1.5.1",
  "tqdm",
  "umap-learn",
  # DWI dependencies
- "dipy == 1.3.0",
- "fury == 0.7.1",
- "nibabel == 3.0.0",
+ "dipy @ git+https://github.com/scilus/[email protected]#egg=dipy",
+ "fury == 0.8.0",
+ "nibabel == 4.0.0",
  # Git dependencies
- "scilpy @ git+https://github.com/scilus/scilpy@1.2.2",
+ "scilpy @ git+https://github.com/scilus/scilpy@1.5.0",
 ]
 description = "Tractography learning"
 dynamic = ["version"]
@@ -48,16 +48,16 @@ maintainers = [
 ]
 name = "tractolearn"
 readme = "README.md"
-requires-python = ">=3.8"
+requires-python = ">=3.10"
 
 [project.optional-dependencies]
 test = [
  "hypothesis >= 6.8.0",
- "pytest == 5.3",
+ "pytest == 7.2.0",
  "pytest-cov",
  "pytest-pep8",
  "pytest-xdist",
- "pytest_console_scripts",
+ "pytest_console_scripts == 1.3.0",
 ]
 dev = [
  "black == 22.12",
@@ -86,7 +86,7 @@ repository = "https://github.com/scil-vital/tractolearn"
 
 [tool.black]
 line-length = 79
-target-version = ["py38"]
+target-version = ["py310"]
 exclude ='''
 (
  /(

tox.ini

@@ -1,5 +1,5 @@
 [tox]
-envlist = py38
+envlist = py310
 isolated_build = True
 
 [testenv]